Opened 11 months ago

Closed 11 months ago

#16339 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: ccaffalett@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.7.6-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000000011ce8e600 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 61)


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{
  "uptime" : 640000,
  "procLaunch" : "2024-11-19 16:00:41.4534 -0500",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,1",
  "procStartAbsTime" : 637899576058883,
  "coalitionID" : 67514,
  "osVersion" : {
    "train" : "macOS 12.7.6",
    "build" : "21H1320",
    "releaseType" : "User"
  },
  "captureTime" : "2024-11-19 16:53:55.5275 -0500",
  "incident" : "20D711A4-60D8-4A22-AD1E-C85CA9A29F9D",
  "bug_type" : "309",
  "pid" : 5553,
  "procExitAbsTime" : 641093558561858,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"50CBB6BD-7B68-58C9-8508-A9CF1854A0EE","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "61E580C7-5D45-4263-2295-2F14C708A704",
  "wakeTime" : 93865,
  "bridgeVersion" : {"build":"21P6074","train":"8.6"},
  "sleepWakeUUID" : "A4CAA0E8-79F7-4115-9E5A-08C37BAA8813",
  "sip" : "enabled",
  "vmRegionInfo" : "0x119b6f569138 is not in any region.  Bytes after previous region: 19352295485753  Bytes before following region: 86193830719176\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      VM_ALLOCATE                 19f03e000-1a0a3e000    [ 26.0M] rw-\/rwx SM=PRV  \n--->  GAP OF 0x5ffe5f5c2000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000119b6f569138","rawCodes":[1,19359285547320],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000119b6f569138"},
  "vmregioninfo" : "0x119b6f569138 is not in any region.  Bytes after previous region: 19352295485753  Bytes before following region: 86193830719176\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      VM_ALLOCATE                 19f03e000-1a0a3e000    [ 26.0M] rw-\/rwx SM=PRV  \n--->  GAP OF 0x5ffe5f5c2000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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  "uuid" : "246818c3-4b9f-3462-bcaf-fdf71975e5fe"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=34.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=34.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1280K       10 \nActivity Tracing                   256K        1 \nCG backing stores                 2688K        4 \nCG image                           684K       55 \nColorSync                          232K       28 \nCoreAnimation                     3036K      127 \nCoreGraphics                        12K        2 \nCoreServices                       220K        1 \nCoreUI image data                 5184K       37 \nFoundation                          36K        2 \nIOKit                             15.5M        2 \nKernel Alloc Once                    8K        1 \nMALLOC                            32.0G      799 \nMALLOC guard page                   48K       11 \nMALLOC_LARGE (reserved)          128.0M        1         reserved VM address space (unallocated)\nMALLOC_MEDIUM (reserved)           1.4G       15         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        204K       51 \nStack                            176.4M       52 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      452.0M      308 \n__CTF                               756        1 \n__DATA                            52.3M      709 \n__DATA_CONST                      42.4M      404 \n__DATA_DIRTY                      1778K      228 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       677.8M      162 \n__OBJC_RO                         82.9M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                           878.2M      710 \n__UNICODE                          592K        1 \ndyld private memory               1056K        3 \nmapped file                      485.5M       62 \nshared memory                     2984K       27 \n===========                     =======  ======= \nTOTAL                             36.6G     3827 \nTOTAL, minus reserved VM space    34.9G     3827 \n",
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}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open pdb:7N9F

Summary of feedback from opening 7N9F fetched from pdb  
---  
note | Fetching compressed mmCIF 7n9f from http://files.rcsb.org/download/7n9f.cif  
  
7n9f title:  
Structure of the in situ yeast NPC [more info...]  
  
Chain information for 7n9f #1  
---  
Chain | Description | UniProt  
0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502  
1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391  
5 6 | orphans bound to Nup192 NTD |   
A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823  
B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541  
C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472  
M O | Nucleoporin NUP192 | NU192_YEAST 1-1683  
N P | Nucleoporin NUP188 | NU188_YEAST 1-1655  
Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839  
U W | Nucleoporin NUP53 | NUP53_YEAST 1-475  
V X | Nucleoporin ASM4 | NUP59_YEAST 1-528  
a h | Nucleoporin NUP120 | NU120_YEAST 1-1037  
b i | Nucleoporin NUP85 | NUP85_YEAST 1-744  
c j | Nucleoporin 145c | NU145_YEAST 0-797  
d k | Protein transport protein SEC13 | SEC13_YEAST 1-297  
e l | Nucleoporin SEH1 | SEH1_YEAST 1-349  
f m | Nucleoporin NUP84 | NUP84_YEAST 1-726  
g n | Nucleoporin NUP133 | NU133_YEAST 1-1157  
o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92  
u v | Nucleoporin NUP82 | NUP82_YEAST 1-713  
w x | Nucleoporin NUP159 | NU159_YEAST 1-1460  
  
7n9f mmCIF Assemblies  
---  
1| complete point assembly  
2| point asymmetric unit  
3| point asymmetric unit, std point frame  
  

> open /Users/chris/Library/CloudStorage/OneDrive-
> rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_44377.map

Opened emd_44377.map as #2, grid size 224,224,224, pixel 10, shown at level
602, step 1, values float32  

> ui tool show "Side View"

> volume #2 level 554.8

> volume #2 level 534

> open /Users/chris/Library/CloudStorage/OneDrive-
> rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/2024_1115_ChimeraX_Session_to_determine_a_plan.cxs

> surface cap true

Opened emd_24258.map as #2, grid size 320,320,320, pixel 6.74, shown at level
2.25e+03, step 1, values float32  
Opened emd_44377.map as #3, grid size 224,224,224, pixel 10, shown at level
556, step 1, values float32  

> surface cap false

opened ChimeraX session  

> select add #4

1703696 atoms, 1734208 bonds, 2080 pseudobonds, 216568 residues, 2 models
selected  

> select subtract #4

Nothing selected  

> select add #4

1703696 atoms, 1734208 bonds, 2080 pseudobonds, 216568 residues, 2 models
selected  

> open pdb:8tie

8tie title:  
Double nuclear outer ring of Nup84-complexes from the yeast NPC [more info...]  
  
Chain information for 8tie #1  
---  
Chain | Description | UniProt  
a l | Nucleoporin NUP120 | NU120_YEAST 1-1037  
b m | Nucleoporin NUP85 | NUP85_YEAST 1-744  
c n | NUP145 isoform 1 | A0A8H4C085_YEASX -605-711  
d o | Protein transport protein SEC13 | SEC13_YEAST 1-297  
e p | Nucleoporin Seh1 |   
f q | Nucleoporin NUP84 | NUP84_YEAST 1-726  
g r | NUP133 isoform 1 | A0A6V8RYD2_YEASX 1-1157  
  

> select add #1

1780317 atoms, 1812453 bonds, 2084 pseudobonds, 226047 residues, 4 models
selected  

> select subtract #4

76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-1064.2,0,1,0,-708.55,0,0,1,-83.832

> view matrix models
> #1,0.97542,0.0049896,0.2203,-1221.2,-0.080623,-0.92234,0.37787,418.73,0.20508,-0.38634,-0.89927,1517.8

> view matrix models
> #1,0.75624,-0.50525,0.41572,-783.85,-0.62498,-0.74585,0.23044,1010,0.19364,-0.43408,-0.87982,1547.8

> view matrix models
> #1,0.74417,-0.51523,0.42514,-771.38,-0.60474,-0.78997,0.10118,1124.6,0.28372,-0.33239,-0.89945,1394.2

> view matrix models
> #1,0.74417,-0.51523,0.42514,-604.67,-0.60474,-0.78997,0.10118,1034.4,0.28372,-0.33239,-0.89945,451.85

> view matrix models
> #1,0.74417,-0.51523,0.42514,-630.3,-0.60474,-0.78997,0.10118,1058,0.28372,-0.33239,-0.89945,456.09

> view matrix models
> #1,0.74417,-0.51523,0.42514,-612.4,-0.60474,-0.78997,0.10118,1062.6,0.28372,-0.33239,-0.89945,455.92

> view matrix models
> #1,0.74417,-0.51523,0.42514,-475.63,-0.60474,-0.78997,0.10118,753.88,0.28372,-0.33239,-0.89945,456.16

> view matrix models
> #1,0.80292,-0.57464,0.15844,-279.81,-0.58923,-0.80534,0.065148,777.21,0.090162,-0.14567,-0.98522,606.72

> view matrix models
> #1,0.62119,-0.76659,0.16265,49.835,-0.78094,-0.62282,0.0471,873.29,0.065195,-0.15628,-0.98556,641.7

> view matrix models
> #1,0.62119,-0.76659,0.16265,42.361,-0.78094,-0.62282,0.0471,870.61,0.065195,-0.15628,-0.98556,640.89

> view matrix models
> #1,0.61546,-0.77233,0.15722,57.084,-0.77997,-0.62552,-0.019516,925.96,0.11342,-0.11062,-0.98737,557.68

> view matrix models
> #1,0.61617,-0.7794,0.11348,97.069,-0.77246,-0.62613,-0.10609,989.06,0.15375,-0.022291,-0.98786,452.09

> view matrix models
> #1,0.68045,-0.72185,0.12616,-23.866,-0.71462,-0.69177,-0.10375,970.04,0.16217,-0.019557,-0.98657,439.92

> view matrix models
> #1,0.70218,-0.70758,0.079176,-19.156,-0.71198,-0.69715,0.084006,817.25,-0.0042435,-0.11536,-0.99331,694.35

> view matrix models
> #1,0.70218,-0.70758,0.079176,-12.898,-0.71198,-0.69715,0.084006,821.71,-0.0042435,-0.11536,-0.99331,695.13

> ui tool show "Fit in Map"

> fitmap #1 inMap #3

Fit molecule 8tie (#1) to map emd_44377.map (#3) using 76621 atoms  
average map value = 561.1, steps = 76  
shifted from previous position = 17.5  
rotated from previous position = 9.23 degrees  
atoms outside contour = 31152, contour level = 556.13  
  
Position of 8tie (#1) relative to emd_44377.map (#3) coordinates:  
Matrix rotation and translation  
0.73322863 -0.67628301 -0.07083110 1175.40549284  
-0.66782038 -0.73580988 0.11224856 1879.70676416  
-0.12803001 -0.03500141 -0.99115246 1909.31002321  
Axis -0.93080882 0.36157055 0.05349465  
Axis point 0.00000000 1209.12640343 946.03248590  
Rotation angle (degrees) 175.46328733  
Shift along axis -312.29331154  
  

> hide #!1 models

> show #!2 models

> hide #!3 models

> volume #2 level 1988

> volume #2 level 1981

> show #!1 models

> hide #!2 models

> show #!3 models

> color zone #3 near sel & #1 distance 60

> surface cap true

> surface cap true color black

Expected a keyword  

> surface cap color black

Expected true or false or a keyword  

> ui tool show "Surface Color"

> color radial #3.1.1 palette #ff0000:#ffffff:#0000ff

> select add #3.1.1

76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 3 models selected  

> select subtract #3.1.1

76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 2 models selected  

> select add #3.1

76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 4 models selected  

> select subtract #3.1

76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 2 models selected  

> color #3.1.1 black

> view matrix models
> #1,0.73685,-0.67227,-0.071412,66.927,-0.66383,-0.73948,0.11178,854.87,-0.12796,-0.034962,-0.99116,560.47

> view matrix models
> #1,0.73685,-0.67227,-0.071412,70.299,-0.66383,-0.73948,0.11178,864.49,-0.12796,-0.034962,-0.99116,475.83

> view matrix models
> #1,0.73685,-0.67227,-0.071412,70.055,-0.66383,-0.73948,0.11178,860.1,-0.12796,-0.034962,-0.99116,490.09

> hide #!3 models

> hide #3.1 models

> hide #!4 models

> show #!3 models

> hide #!1 models

> select subtract #1

Nothing selected  

> show #3.1 models

> hide #!3 models

> show #!3 models

> color #3.1.1 black

> hide #!3 models

> show #!3 models

> hide #!3.1 models

> show #3.1 models

> close session

> open /Users/chris/Library/CloudStorage/OneDrive-
> rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_44377.map format ccp4

Opened emd_44377.map as #1, grid size 224,224,224, pixel 10, shown at level
602, step 1, values float32  

> ui mousemode right "map eraser"

> volume erase #1 center 1514.4,1228.8,362.34 radius 226.97

Opened emd_44377.map copy as #3, grid size 224,224,224, pixel 10, shown at
step 1, values float32  

> volume erase #3 center 1534.5,1291.9,545.55 radius 226.24

> volume copy #3 subregion 130,106,31,177,153,78

Opened emd_44377.map copy as #4, grid size 48,48,48, pixel 10, shown at step
1, values float32  

> close session

> open /Users/chris/Library/CloudStorage/OneDrive-
> rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_44377.map format ccp4

Opened emd_44377.map as #1, grid size 224,224,224, pixel 10, shown at level
602, step 1, values float32  

> volume #1 level 540.4

> ui mousemode right "map eraser"

> volume erase #1 center 1589.9,468.34,1013.5 radius 549.55

Opened emd_44377.map copy as #3, grid size 224,224,224, pixel 10, shown at
step 1, values float32  

> volume erase #3 center 989.98,550.2,933.02 radius 548.8

> volume erase #3 center 680.19,716.28,1018.8 radius 548.8

> volume erase #3 center 710.86,642.99,1406.6 radius 548.8

> volume erase #3 center 1143,492.49,1462.9 radius 548.8

> volume erase #3 center 1036.5,681.56,389.54 radius 548.8

> volume erase #3 center 799.64,670.44,449.72 radius 548.8

> volume erase #3 center 1165.8,955.81,170.69 radius 599.2

> color #3.1.1 black

> surface cap true

> color #3.1.1 black

> color #3.1.1 white

> volume erase #3 center 1801,765.51,1081.1 radius 599.2

> hide #!3 models

> show #!1 models

> hide #3.1 models

> open /Users/chris/Library/CloudStorage/OneDrive-
> rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/8tie-assembly1.cif

8tie-assembly1.cif title:  
Double nuclear outer ring of Nup84-complexes from the yeast NPC [more info...]  
  
Chain information for 8tie-assembly1.cif #4  
---  
Chain | Description  
a l | Nucleoporin NUP120  
b m | Nucleoporin NUP85  
c n | NUP145 isoform 1  
d o | Protein transport protein SEC13  
e p | Nucleoporin Seh1  
f q | Nucleoporin NUP84  
g r | NUP133 isoform 1  
  

> open pdb:7n9f

7n9f title:  
Structure of the in situ yeast NPC [more info...]  
  
Chain information for 7n9f #5  
---  
Chain | Description | UniProt  
0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502  
1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391  
5 6 | orphans bound to Nup192 NTD |   
A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823  
B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541  
C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472  
M O | Nucleoporin NUP192 | NU192_YEAST 1-1683  
N P | Nucleoporin NUP188 | NU188_YEAST 1-1655  
Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839  
U W | Nucleoporin NUP53 | NUP53_YEAST 1-475  
V X | Nucleoporin ASM4 | NUP59_YEAST 1-528  
a h | Nucleoporin NUP120 | NU120_YEAST 1-1037  
b i | Nucleoporin NUP85 | NUP85_YEAST 1-744  
c j | Nucleoporin 145c | NU145_YEAST 0-797  
d k | Protein transport protein SEC13 | SEC13_YEAST 1-297  
e l | Nucleoporin SEH1 | SEH1_YEAST 1-349  
f m | Nucleoporin NUP84 | NUP84_YEAST 1-726  
g n | Nucleoporin NUP133 | NU133_YEAST 1-1157  
o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92  
u v | Nucleoporin NUP82 | NUP82_YEAST 1-713  
w x | Nucleoporin NUP159 | NU159_YEAST 1-1460  
  
7n9f mmCIF Assemblies  
---  
1| complete point assembly  
2| point asymmetric unit  
3| point asymmetric unit, std point frame  
  

> select #5:0

Nothing selected  

> select #5/0

8762 atoms, 8935 bonds, 16 pseudobonds, 1085 residues, 2 models selected  

> select #5/0,l

11200 atoms, 11434 bonds, 17 pseudobonds, 1392 residues, 2 models selected  

> hide #!1 models

> select ~sel & ##selected

201762 atoms, 205342 bonds, 243 pseudobonds, 25679 residues, 2 models selected  

> select #5:0,Y

Nothing selected  

> select #5:0,Y

Nothing selected  

> select #5:0

Nothing selected  

> select #5/0

8762 atoms, 8935 bonds, 16 pseudobonds, 1085 residues, 2 models selected  

> select #5/0,Y

17532 atoms, 17878 bonds, 32 pseudobonds, 2171 residues, 2 models selected  

> select #5/0,

Expected an objects specifier or a keyword  

> select #5/0

8762 atoms, 8935 bonds, 16 pseudobonds, 1085 residues, 2 models selected  

> open /Users/chris/Library/CloudStorage/OneDrive-
> rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx-
> GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/7n9f-assembly1.cif

7n9f-assembly1.cif title:  
Structure of the in situ yeast NPC [more info...]  
  
Chain information for 7n9f-assembly1.cif #6  
---  
Chain | Description  
0 0-2 0-3 0-4 0-5 0-6 0-7 0-8 Y Y-2 Y-3 Y-4 Y-5 Y-6 Y-7 Y-8 | Nucleoporin NUP170  
1 1-2 1-3 1-4 1-5 1-6 1-7 1-8 Z Z-2 Z-3 Z-4 Z-5 Z-6 Z-7 Z-8 | Nucleoporin NUP157  
5 5-2 5-3 5-4 5-5 5-6 5-7 5-8 6 6-2 6-3 6-4 6-5 6-6 6-7 6-8 | orphans bound to Nup192 NTD  
A A-2 A-3 A-4 A-5 A-6 A-7 A-8 D D-2 D-3 D-4 D-5 D-6 D-7 D-8 G G-2 G-3 G-4 G-5 G-6 G-7 G-8 J J-2 J-3 J-4 J-5 J-6 J-7 J-8 y y-2 y-3 y-4 y-5 y-6 y-7 y-8 z z-2 z-3 z-4 z-5 z-6 z-7 z-8 | Nucleoporin NSP1  
B B-2 B-3 B-4 B-5 B-6 B-7 B-8 E E-2 E-3 E-4 E-5 E-6 E-7 E-8 H H-2 H-3 H-4 H-5 H-6 H-7 H-8 K K-2 K-3 K-4 K-5 K-6 K-7 K-8 | Nucleoporin NUP57  
C C-2 C-3 C-4 C-5 C-6 C-7 C-8 F F-2 F-3 F-4 F-5 F-6 F-7 F-8 I I-2 I-3 I-4 I-5 I-6 I-7 I-8 L L-2 L-3 L-4 L-5 L-6 L-7 L-8 | Nucleoporin NUP49/NSP49  
M M-2 M-3 M-4 M-5 M-6 M-7 M-8 O O-2 O-3 O-4 O-5 O-6 O-7 O-8 | Nucleoporin NUP192  
N N-2 N-3 N-4 N-5 N-6 N-7 N-8 P P-2 P-3 P-4 P-5 P-6 P-7 P-8 | Nucleoporin NUP188  
Q Q-2 Q-3 Q-4 Q-5 Q-6 Q-7 Q-8 R R-2 R-3 R-4 R-5 R-6 R-7 R-8 S S-2 S-3 S-4 S-5 S-6 S-7 S-8 T T-2 T-3 T-4 T-5 T-6 T-7 T-8 | Nucleoporin NIC96  
U U-2 U-3 U-4 U-5 U-6 U-7 U-8 W W-2 W-3 W-4 W-5 W-6 W-7 W-8 | Nucleoporin NUP53  
V V-2 V-3 V-4 V-5 V-6 V-7 V-8 X X-2 X-3 X-4 X-5 X-6 X-7 X-8 | Nucleoporin ASM4  
a a-2 a-3 a-4 a-5 a-6 a-7 a-8 h h-2 h-3 h-4 h-5 h-6 h-7 h-8 | Nucleoporin NUP120  
b b-2 b-3 b-4 b-5 b-6 b-7 b-8 i i-2 i-3 i-4 i-5 i-6 i-7 i-8 | Nucleoporin NUP85  
c c-2 c-3 c-4 c-5 c-6 c-7 c-8 j j-2 j-3 j-4 j-5 j-6 j-7 j-8 | Nucleoporin 145c  
d d-2 d-3 d-4 d-5 d-6 d-7 d-8 k k-2 k-3 k-4 k-5 k-6 k-7 k-8 | Protein transport protein SEC13  
e e-2 e-3 e-4 e-5 e-6 e-7 e-8 l l-2 l-3 l-4 l-5 l-6 l-7 l-8 | Nucleoporin SEH1  
f f-2 f-3 f-4 f-5 f-6 f-7 f-8 m m-2 m-3 m-4 m-5 m-6 m-7 m-8 | Nucleoporin NUP84  
g g-2 g-3 g-4 g-5 g-6 g-7 g-8 n n-2 n-3 n-4 n-5 n-6 n-7 n-8 | Nucleoporin NUP133  
o o-2 o-3 o-4 o-5 o-6 o-7 o-8 p p-2 p-3 p-4 p-5 p-6 p-7 p-8 q q-2 q-3 q-4 q-5 q-6 q-7 q-8 r r-2 r-3 r-4 r-5 r-6 r-7 r-8 s s-2 s-3 s-4 s-5 s-6 s-7 s-8 t t-2 t-3 t-4 t-5 t-6 t-7 t-8 | Dynein light chain 1, cytoplasmic  
u u-2 u-3 u-4 u-5 u-6 u-7 u-8 v v-2 v-3 v-4 v-5 v-6 v-7 v-8 | Nucleoporin NUP82  
w w-2 w-3 w-4 w-5 w-6 w-7 w-8 x x-2 x-3 x-4 x-5 x-6 x-7 x-8 | Nucleoporin NUP159  
  

> log metadata #6

Metadata for 7n9f-assembly1.cif #6  
---  
Title | Structure of the in situ yeast NPC  
Citation | Akey, C.W., Singh, D., Ouch, C., Echeverria, I., Nudelman, I., Varberg, J.M., Yu, Z., Fang, F., Shi, Y., Wang, J., Salzberg, D., Song, K., Xu, C., Gumbart, J.C., Suslov, S., Unruh, J., Jaspersen, S.L., Chait, B.T., Sali, A., Fernandez-Martinez, J., Ludtke, S.J., Villa, E., Rout, M.P. (2022). Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell, 185, 361-378.e25. PMID: 34982960. DOI: 10.1016/j.cell.2021.12.015  
Experimental method | Electron microscopy  
  
> select clear


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
      OS Loader Version: 540.120.3~37

Software:

    System Software Overview:

      System Version: macOS 12.7.6 (21H1320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 25 days 18:52

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by pett, 11 months ago

Component: Unassigned → Window Toolkit
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

Reported by Chris Caffalette

comment:2 by Tom Goddard, 11 months ago

Resolution: → duplicate
Status: assigned → closed

ChimeraX crashed due to a bug in the Qt window toolkit. It seems to happen when unplugging or plugging in an external display or when the computer wakes from sleep. The crash report says it is handling some display reconfiguration when it crashes. We don't have any way to fix this right now. I have not even been able to reproduce the crash despite about 100 people reporting it in the last 4 months. It may be that the crash happens less often in the ChimeraX 1.9 release candidate and daily builds with use a newer version of Qt (6.7 instead of 6.6) but we have still seen some reports of the same crash in the newer versions.

If you remember what you were doing just before it crashed that might help me figure out how to reproduce it on my machine and find a fix.

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